diff options
Diffstat (limited to 'sci-biology/qrna/files/qrna-2.0.4-ldflags.patch')
-rw-r--r-- | sci-biology/qrna/files/qrna-2.0.4-ldflags.patch | 381 |
1 files changed, 381 insertions, 0 deletions
diff --git a/sci-biology/qrna/files/qrna-2.0.4-ldflags.patch b/sci-biology/qrna/files/qrna-2.0.4-ldflags.patch new file mode 100644 index 000000000000..c53b56b0e935 --- /dev/null +++ b/sci-biology/qrna/files/qrna-2.0.4-ldflags.patch @@ -0,0 +1,381 @@ +diff --git a/squid/Makefile b/squid/Makefile +index fafab4c..8c329b3 100644 +--- a/squid/Makefile ++++ b/squid/Makefile +@@ -19,7 +19,6 @@ MANDIR = $(HOME)/man + # On an Alliant, use fxc. + # + #CC = cc +-CC = gcc + #CC = fxc + + ## Any special compiler flags you want. +@@ -37,7 +36,6 @@ CC = gcc + # for instance. If the code builds cleanly but seg faults, try + # rebuilding without optimization. + # +-CFLAGS = -O -m32 + #CFLAGS = -g + #CFLAGS = -TARG:exc_max -64 -Ofast=ip27 #specific SGI Origin200 compiler# + +@@ -47,8 +45,6 @@ CFLAGS = -O -m32 + # Don't worry. The Makefile tests for ranlib existence and will work + # fine on SGIs even if RANLIB is set. + # +-AR = ar rcv +-RANLIB = ranlib + + ## Machine specific definitions + # +@@ -108,41 +104,41 @@ DIST = $(SRC) $(HDRS) $(READMES) Makefile + all: $(LIBTARGET) + + alistat: $(OBJ) alistat_main.o +- $(CC) $(CFLAGS) $(MDEFS) -o alistat $(OBJ) alistat_main.o $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o alistat $(OBJ) alistat_main.o $(LIBS) + + compalign: $(OBJ) compalign_main.o +- $(CC) $(CFLAGS) $(MDEFS) -o compalign $(OBJ) compalign_main.o $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o compalign $(OBJ) compalign_main.o $(LIBS) + + compstruct: $(OBJ) compstruct_main.o +- $(CC) $(CFLAGS) $(MDEFS) -o compstruct $(OBJ) compstruct_main.o $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o compstruct $(OBJ) compstruct_main.o $(LIBS) + + getseq: $(OBJ) getseq_main.o +- $(CC) $(CFLAGS) $(MDEFS) -o getseq $(OBJ) getseq_main.o $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o getseq $(OBJ) getseq_main.o $(LIBS) + + reformat: $(OBJ) reformat_main.o +- $(CC) $(CFLAGS) $(MDEFS) -o reformat $(OBJ) reformat_main.o $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o reformat $(OBJ) reformat_main.o $(LIBS) + + revcomp: $(OBJ) revcomp_main.o +- $(CC) $(CFLAGS) $(MDEFS) -o revcomp $(OBJ) revcomp_main.o $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o revcomp $(OBJ) revcomp_main.o $(LIBS) + + seqstat: $(OBJ) seqstat_main.o +- $(CC) $(CFLAGS) $(MDEFS) -o seqstat $(OBJ) seqstat_main.o $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o seqstat $(OBJ) seqstat_main.o $(LIBS) + + seqsplit: $(OBJ) seqsplit_main.o +- $(CC) $(CFLAGS) $(MDEFS) -o seqstat $(OBJ) seqsplit_main.o $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o seqstat $(OBJ) seqsplit_main.o $(LIBS) + + shuffle: $(OBJ) shuffle_main.o +- $(CC) $(CFLAGS) $(MDEFS) -o shuffle $(OBJ) shuffle_main.o $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o shuffle $(OBJ) shuffle_main.o $(LIBS) + + translate: $(OBJ) translate_main.o +- $(CC) $(CFLAGS) $(MDEFS) -o translate $(OBJ) translate_main.o $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o translate $(OBJ) translate_main.o $(LIBS) + + weight: $(OBJ) weight_main.o +- $(CC) $(CFLAGS) $(MDEFS) -o weight $(OBJ) weight_main.o $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o weight $(OBJ) weight_main.o $(LIBS) + + + $(LIBTARGET): $(OBJ) +- $(AR) $(LIBTARGET) $(OBJ) ++ $(AR) rcv $(LIBTARGET) $(OBJ) + -if test -x /bin/ranlib; then /bin/ranlib $(LIBTARGET); else exit 0; fi + -if test -x /usr/bin/ranlib; then /usr/bin/ranlib $(LIBTARGET); else exit 0; fi + -if test -x $(RANLIB); then $(RANLIB) $(LIBTARGET); else exit 0; fi +@@ -182,4 +178,4 @@ tags: + etags -t $(SRC) $(HDRS) + + .c.o: +- $(CC) $(CFLAGS) $(MDEFS) -c $< ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -c $< +diff --git a/squid02/Makefile b/squid02/Makefile +index d32240f..757e0dd 100644 +--- a/squid02/Makefile ++++ b/squid02/Makefile +@@ -27,8 +27,6 @@ SCRIPTDIR = ${exec_prefix}/bin + + ## your compiler and compiler flags + # +-CC = gcc +-CFLAGS = -g -O2 -m32 + + ## other defined flags for machine-specific stuff + # +@@ -37,8 +35,6 @@ LIBS = -lm + + ## Archiver command + # +-AR = ar rcv +-RANLIB = ranlib + + ## instructions for installing man pages + # +@@ -158,10 +154,10 @@ OBJS = a2m.o\ + all: version.h $(PROGS) libsquid.a + + $(PROGS): %: %_main.o version.h $(OBJS) +- $(CC) $(CFLAGS) $(MDEFS) $(PVMLIBDIR) -o $@ $@_main.o $(OBJS) $(PVMLIBS) $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) $(PVMLIBDIR) -o $@ $@_main.o $(OBJS) $(PVMLIBS) $(LIBS) + + .c.o: +- $(CC) $(CFLAGS) $(PVMFLAG) $(PVMINCDIR) $(MDEFS) -c $< ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(PVMFLAG) $(PVMINCDIR) $(MDEFS) -c $< + ################################################################ + + +@@ -172,7 +168,7 @@ $(PROGS): %: %_main.o version.h $(OBJS) + module: libsquid.a + + libsquid.a: version.h $(OBJS) +- $(AR) libsquid.a $(OBJS) ++ $(AR) rcv libsquid.a $(OBJS) + $(RANLIB) libsquid.a + chmod 644 libsquid.a + ################################################################# +diff --git a/src/Makefile b/src/Makefile +index d93182b..35c8b3d 100644 +--- a/src/Makefile ++++ b/src/Makefile +@@ -21,7 +21,6 @@ SQUIDDIR02 = ../squid02 + SQUIDSRCDIR02 = ../squid02 + + ## your compiler +-CC = gcc + #CC = cc + + ## any special compiler flags you want +@@ -30,7 +29,6 @@ CC = gcc + #CFLAGS = -g -Wall -pedantic + #CFLAGS = -TARG:exc_max + #CFLAGS = -g -fullwarn -wlint,-fviah +-CFLAGS = -O -m32 + #CFLAGS = -p # profiling # + #CFLAGS = -64 -Ofast=ip27 #specific warhorse compiler# + +@@ -131,145 +129,145 @@ DEMOS = + all: $(PROGS) + + main: $(OBJ) main.o +- $(CC) $(CFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(LIBS) + cfgbuild: $(OBJ) cfgbuild.o +- $(CC) $(CFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(OBJ) $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(OBJ) $(LIBS) + eqrna: $(OBJ) eqrna.o +- $(CC) $(CFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(OBJ) $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(OBJ) $(LIBS) + eqrna_sample: $(OBJ) eqrna_sample.o +- $(CC) $(CFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(OBJ) $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(OBJ) $(LIBS) + shuffle: $(OBJ) shuffle.o +- $(CC) $(CFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(OBJ) $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(OBJ) $(LIBS) + rnamat_main: $(OBJ2) rnamat_main.o +- $(CC) $(CFLAGS) -o $@ -L$(SQUIDDIR02) $@.o $(OBJ2) $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ -L$(SQUIDDIR02) $@.o $(OBJ2) $(LIBS) + + main.o: ../src/main.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + cfgbuild.o: ../src/cfgbuild.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + eqrna.o: ../src/eqrna.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + eqrna_sample.o: ../src/eqrna_sample.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + shuffle.o: ../src/shuffle.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + rnamat_main.o: ../src/rnamat_main.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR02) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR02) -c $? + + cfgio.o: ../src/cfgio.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + cfgmodel.o: ../src/cfgmodel.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + cfgparse.o: ../src/cfgparse.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + codcreatealign.o: ../src/codcreatealign.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + coddp.o: ../src/coddp.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + coddpscanfast.o: ../src/coddpscanfast.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + codmodel.o: ../src/codmodel.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + codon.o: ../src/codon.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + codscorealign.o: ../src/codscorealign.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + er_math.o: ../src/er_math.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + er_vectop.o: ../src/er_vectop.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR02) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR02) -c $? + evd.o: ../src/evd.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + evolcodmodel.o: ../src/evolcodmodel.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + evolemissions.o: ../src/evolemissions.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + evolmisc.o: ../src/evolmisc.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + evolnullmodel.o: ../src/evolnullmodel.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + evolothmodel.o: ../src/evolothmodel.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + evolqrnaversion.o: ../src/evolqrnaversion.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + evolscorewithmodels.o: ../src/evolscorewithmodels.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + evolscorewithmodelscanfast.o: ../src/evolscorewithmodelscanfast.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + evolriboprob.o: ../src/evolriboprob.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + evolrnadp.o: ../src/evolrnadp.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + evolrnadpscanfast.o: ../src/evolrnadpscanfast.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + evolrnamodel.o: ../src/evolrnamodel.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + evolrnascorealign.o: ../src/evolrnascorealign.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + evolve.o: ../src/evolve.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + globals.o: ../src/globals.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + hexamer.o: ../src/hexamer.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + matrix.o: ../src/matrix.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + misc.o: ../src/misc.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + nrnscfg.o: ../src/nrnscfg.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + nstack.o: ../src/nstack.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR02) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR02) -c $? + nullmodel.o: ../src/nullmodel.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + othcreatealign.o: ../src/othcreatealign.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + othdp.o: ../src/othdp.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + othdpscanfast.o: ../src/othdpscanfast.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + othmodel.o: ../src/othmodel.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + othscorealign.o: ../src/othscorealign.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + posterior.o: ../src/posterior.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + qrnaversion.o: ../src/qrnaversion.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + riboprob.o: ../src/riboprob.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + rnacreatealign.o: ../src/rnacreatealign.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + rnadp.o: ../src/rnadp.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + rnadpscanfast.o: ../src/rnadpscanfast.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + rnaio.o: ../src/rnaio.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + rnamat.o: ../src/rnamat.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR02) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR02) -c $? + rnamodel.o: ../src/rnamodel.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + rnaoutput.o: ../src/rnaoutput.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + rnascorealign.o: ../src/rnascorealign.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + rnascfg.o: ../src/rnascfg.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + rnascfgscanfast.o: ../src/rnascfgscanfast.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + scorewithmodels.o: ../src/scorewithmodels.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + scorewithmodelscanfast.o: ../src/scorewithmodelscanfast.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + seqio.o: ../src/seqio.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + trace.o: ../src/trace.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + traceSCFG.o: ../src/traceSCFG.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + tying.o: ../src/tying.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + + + install: $(PROGS) +@@ -313,10 +311,10 @@ lint: + /usr/lib/lint/llib-lm.ln + + .c.o: +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $< ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $< + + .m.o: +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $< ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $< + + + |